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- PDB-3ap2: Crystal structure of human tyrosylprotein sulfotransferase-2 comp... -

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Basic information

Entry
Database: PDB / ID: 3ap2
TitleCrystal structure of human tyrosylprotein sulfotransferase-2 complexed with PAP,C4 peptide, and phosphate ion
Components
  • C4 peptide
  • Protein-tyrosine sulfotransferase 2
KeywordsTRANSFERASE / sulfotransferase fold
Function / homology
Function and homology information


peptidyl-tyrosine sulfation / protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / Golgi membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Protein-tyrosine sulfotransferase / Sulfotransferase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / PHOSPHATE ION / Protein-tyrosine sulfotransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTeramoto, T. / Fujikawa, Y. / Kawaguchi, Y. / Kurogi, K. / Soejima, M. / Adachi, R. / Nakanishi, Y. / Mishiro-Sato, E. / Liu, M.-C. / Sakakibara, Y. ...Teramoto, T. / Fujikawa, Y. / Kawaguchi, Y. / Kurogi, K. / Soejima, M. / Adachi, R. / Nakanishi, Y. / Mishiro-Sato, E. / Liu, M.-C. / Sakakibara, Y. / Suiko, M. / Kimura, M. / Kakuta, Y.
CitationJournal: To be Published
Title: Crystal structure of human tyrosylprotein sulfotransferase-2: Insights into substrate-binding and catalysis of post-translational protein tyrosine sulfation
Authors: Teramoto, T. / Fujikawa, Y. / Kawaguchi, Y. / Kurogi, K. / Soejima, M. / Adachi, R. / Nakanishi, Y. / Mishiro-Sato, E. / Liu, M.-C. / Sakakibara, Y. / Suiko, M. / Kimura, M. / Kakuta, Y.
History
DepositionOct 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine sulfotransferase 2
B: Protein-tyrosine sulfotransferase 2
S: C4 peptide
T: C4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9458
Polymers77,9044
Non-polymers1,0414
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-29 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.379, 138.379, 228.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABST

#1: Protein Protein-tyrosine sulfotransferase 2 / Tyrosylprotein sulfotransferase 2 / TPST-2


Mass: 37743.656 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 43-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPST2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O60704, protein-tyrosine sulfotransferase
#2: Protein/peptide C4 peptide


Mass: 1208.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis

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Non-polymers , 4 types, 58 molecules

#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium malonate (pH 5.0), 10% polyethylene glycol 3350, 1M sodium/potassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 31865 / Num. obs: 31865 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 13.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1109 / Rsym value: 0.585 / % possible all: 68.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35.49 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.089 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24866 1615 5.1 %RANDOM
Rwork0.20722 ---
obs0.2094 30245 96.22 %-
all-30245 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 65 54 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225160
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9937016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25923.421228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39515913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8751542
X-RAY DIFFRACTIONr_chiral_restr0.1030.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213863
X-RAY DIFFRACTIONr_mcbond_it0.6831.53125
X-RAY DIFFRACTIONr_mcangle_it1.28225070
X-RAY DIFFRACTIONr_scbond_it2.01632035
X-RAY DIFFRACTIONr_scangle_it3.2594.51931
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 89 -
Rwork0.275 1590 -
obs--69.38 %

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